Variant report

Variant	rs11634818
Chromosome Location	chr15:62356386-62356387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr15:62355756-62356709	Hela-S3	cervix:	n/a	chr15:62356060-62356077
2	GTF2F1	chr15:62355690-62356616	Hela-S3	cervix:	n/a	n/a
3	FOS	chr15:62355985-62356826	MCF10A-Er-Src	breast:	n/a	chr15:62356372-62356383
4	POLR2A	chr15:62355714-62356421	Hela-S3	cervix:	n/a	n/a
5	NFYB	chr15:62355669-62356438	Hela-S3	cervix:	n/a	n/a
6	GTF3C2	chr15:62355858-62356405	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:62355672-62356822	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr15:62355953-62356689	MCF10A-Er-Src	breast:	n/a	n/a
9	TBP	chr15:62355998-62356735	Hela-S3	cervix:	n/a	n/a
10	NFYA	chr15:62356100-62356714	Hela-S3	cervix:	n/a	n/a
11	MAFK	chr15:62355815-62356806	Hela-S3	cervix:	n/a	chr15:62356675-62356685 chr15:62356671-62356682
12	STAT3	chr15:62355955-62356805	MCF10A-Er-Src	breast:	n/a	n/a
13	JUND	chr15:62355856-62356555	Hela-S3	cervix:	n/a	chr15:62355966-62355975
14	FOS	chr15:62356097-62356572	HUVEC	blood vessel:	n/a	chr15:62356372-62356383
15	ELK4	chr15:62355996-62356410	Hela-S3	cervix:	n/a	n/a
16	MYC	chr15:62356005-62356849	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr15:62356074-62356798	MCF10A-Er-Src	breast:	n/a	chr15:62356372-62356383
18	RCOR1	chr15:62355989-62356732	Hela-S3	cervix:	n/a	n/a
19	MAFK	chr15:62356350-62356714	HepG2	liver:	n/a	chr15:62356675-62356685 chr15:62356671-62356682
20	MAX	chr15:62355941-62356863	Hela-S3	cervix:	n/a	n/a
21	CEBPB	chr15:62355960-62356495	Hela-S3	cervix:	n/a	n/a
22	SMC3	chr15:62356062-62356500	Hela-S3	cervix:	n/a	n/a
23	MAFK	chr15:62356332-62356779	HepG2	liver:	n/a	chr15:62356675-62356685 chr15:62356671-62356682
24	MYC	chr15:62355996-62356860	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr15:62356045-62356788	Hela-S3	cervix:	n/a	n/a
26	EP300	chr15:62355870-62356642	Hela-S3	cervix:	n/a	chr15:62355964-62355978 chr15:62355968-62355977 chr15:62355902-62355916
27	FOS	chr15:62356147-62356623	Hela-S3	cervix:	n/a	chr15:62356372-62356383
28	FOS	chr15:62356055-62356856	MCF10A-Er-Src	breast:	n/a	chr15:62356372-62356383
29	USF2	chr15:62356063-62356688	Hela-S3	cervix:	n/a	n/a
30	MAX	chr15:62355915-62356830	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr15:62356029-62356616	MCF10A-Er-Src	breast:	n/a	n/a
32	MXI1	chr15:62355959-62356708	Hela-S3	cervix:	n/a	n/a
33	STAT3	chr15:62355841-62356688	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr15:62355919-62356595	Hela-S3	cervix:	n/a	n/a
35	FOS	chr15:62355903-62356843	MCF10A-Er-Src	breast:	n/a	chr15:62355966-62355975 chr15:62356372-62356383
36	STAT3	chr15:62355888-62356818	MCF10A-Er-Src	breast:	n/a	n/a
37	GATA3	chr15:62356376-62356824	MCF-7	breast:	n/a	n/a
38	MAFK	chr15:62356277-62356798	IMR90	lung:	n/a	chr15:62356675-62356685 chr15:62356671-62356682

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62351333..62353521-chr15:62354960..62356532,2	MCF-7	breast:
2	chr15:62352901..62356622-chr15:62357854..62362137,6	K562	blood:

Variant related genes	Relation type
VPS13C	TF binding region
C2CD4A	TF binding region
ENSG00000129003	Chromatin interaction
ENSG00000259251	Chromatin interaction
ENSG00000198535	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10519155	1.00[ASN][1000 genomes]
rs10519156	1.00[ASN][1000 genomes]
rs11629598	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs11629645	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11629741	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11631273	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11633932	1.00[ASN][1000 genomes]
rs11634077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11634306	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11634312	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11636682	1.00[ASN][1000 genomes]
rs11637599	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11637606	1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs11637693	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11639286	0.83[AMR][1000 genomes]
rs12148573	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12901055	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs12907567	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs12909386	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12909673	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12911068	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911422	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12913358	0.84[EUR][1000 genomes]
rs12916410	0.89[AMR][1000 genomes]
rs12917339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12917444	1.00[ASN][1000 genomes]
rs17271312	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17271389	1.00[ASN][1000 genomes]
rs17303894	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs2303405	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs34017665	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34042779	0.83[AMR][1000 genomes]
rs34088392	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34173668	0.83[AMR][1000 genomes]
rs34282385	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34311301	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34338090	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34391931	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34546531	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34933463	0.82[EUR][1000 genomes]
rs34958705	0.83[AMR][1000 genomes]
rs35119291	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35168171	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35324423	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35577653	1.00[ASN][1000 genomes]
rs35785804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35932993	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36126734	0.83[AMR][1000 genomes]
rs36175042	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4143844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs4143845	0.89[AMR][1000 genomes]
rs62006969	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62007448	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62007453	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007454	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007455	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62007767	1.00[ASN][1000 genomes]
rs62008531	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008549	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv1560	chr15:62354264-62399304	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11634818	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62353400-62358800	Weak transcription	Placenta	Placenta
2	chr15:62353400-62358800	Weak transcription	Psoas Muscle	Psoas
3	chr15:62353400-62358800	Weak transcription	Stomach Mucosa	stomach
4	chr15:62353400-62359000	Weak transcription	Lung	lung
5	chr15:62353600-62356400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:62353600-62356400	Weak transcription	K562	blood
7	chr15:62353600-62358400	Weak transcription	Aorta	Aorta
8	chr15:62353600-62358600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:62353600-62358800	Weak transcription	Liver	Liver
10	chr15:62353600-62358800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:62353600-62358800	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:62353600-62358800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:62353800-62358800	Weak transcription	Adipose Nuclei	Adipose
14	chr15:62354000-62358600	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:62354000-62358800	Weak transcription	Brain Angular Gyrus	brain
16	chr15:62354200-62358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:62354200-62358800	Weak transcription	Brain Anterior Caudate	brain
18	chr15:62354400-62358600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:62354400-62358600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:62355600-62357000	Flanking Active TSS	Hela-S3	cervix
21	chr15:62355600-62357200	Enhancers	Pancreas	Pancrea
22	chr15:62355600-62357400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:62355600-62357400	Bivalent Enhancer	Fetal Intestine Large	intestine
24	chr15:62355600-62357400	Enhancers	Fetal Intestine Small	intestine
25	chr15:62355600-62357600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:62355800-62356400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr15:62355800-62356600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:62355800-62356600	Flanking Active TSS	HMEC	breast
29	chr15:62355800-62357200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr15:62356000-62356400	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr15:62356000-62356400	Flanking Active TSS	HUVEC	blood vessel
32	chr15:62356000-62356600	Enhancers	HSMM	muscle
33	chr15:62356000-62356600	Flanking Active TSS	NHEK	skin
34	chr15:62356000-62356800	Bivalent Enhancer	A549	lung
35	chr15:62356000-62357000	Enhancers	Duodenum Mucosa	Duodenum
36	chr15:62356200-62356600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:62356200-62356600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:62356200-62358800	Weak transcription	Esophagus	oesophagus
39	chr15:62356200-62358800	Weak transcription	Gastric	stomach

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